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Glioblastoma stem cells show transcriptionally correlated spatial organization

1 day 7 hours ago
Glioblastoma (GBM) is an aggressive brain cancer with a poor survival rate. Despite hundreds of clinical trials, there is no effective targeted therapy. Glioblastoma stem cells (GSCs) are an important GBM model system. In culture, these cells form spatial structures that share morphological aspects with their source tumors. We collected 17,000 phase-contrast images of 15 patient-derived GSC lines growing to confluence. We find that GSCs grow in characteristic multicellular patterns depending on...
Shamini Ayyadhury

Organic chemicals of Arctic concern in Russian coastal seas

2 days 7 hours ago
Arctic ecosystems face significant threats from chemicals of global concern. Persistent organic pollutants (POPs) and polycyclic aromatic hydrocarbons (PAHs) have been consistently detected in the Arctic through decades of monitoring. POPs are known to bioaccumulate in food webs, and both POPs and PAHs are toxic posing risks to wildlife and human health. While regular monitoring activities have been implemented in most Arctic countries, information from the Russian Arctic is still limited. This...
Xi-Ze Min

Disseminated pediatric low-grade glioma and hydrocephalus: a multinational consortium analysis of incidence and mortality

2 days 7 hours ago
CONCLUSIONS: This study represents the largest and most comprehensive cohort of patients with DPLGG to date. While histopathology and tumor location were associated with hydrocephalus in this cohort, the dissemination pattern was not directly associated with hydrocephalus incidence but rather the timing of hydrocephalus diagnosis. Hydrocephalus does not impact survival in patients with DPLGG; however, it is associated with worse functional outcomes.
Alexander T Lyons

Proteins in the Genome Browser: integration of phylogenies, alignments, and structures with nucleotide-level evidence in JBrowse 2

3 days 7 hours ago
Recent advances in protein structure prediction have created high-confidence candidate structures for every protein-coding gene in a genome. Concomitantly, many software packages have been created to visualize protein multiple sequence alignments (MSAs), protein structures, and protein annotations. However, few software tools can highlight the direct relationship between nucleotide variation of protein-coding genes in genome space and the evolutionary and structural context of that variation in...
Colin Diesh

CACHE Challenge #3: Targeting the Nsp3 Macrodomain of SARS-CoV-2

3 days 7 hours ago
The third Critical Assessment of Computational Hit-finding Experiments (CACHE) challenged computational teams to identify chemically novel ligands targeting the macrodomain 1 of SARS-CoV-2 Nsp3, a promising coronavirus drug target. Twenty-three groups deployed diverse design strategies to collectively select 1739 ligand candidates. While over 85% of the designed molecules were chemically novel, the best experimentally confirmed hits were structurally similar to previously published compounds....
Oleksandra Herasymenko

SorghumBase: a knowledgebase for sorghum genomics, phenomics, and stakeholder engagement

5 days 7 hours ago
Centralizing valuable community data and resources into a user-friendly interface and accessible repository has become essential for agricultural science; embracing Findable Accessible, Interoperable, and Reusable (FAIR) principles is now standard for effective databases. SorghumBase (https://www.sorghumbase.org) is a knowledgebase designed for the sorghum research community. The SorghumBase team curates genomic, transcriptomic, variation, and phenotypic information and aggregates community...
Nicholas Gladman

Multiomic integration reveals tumoral heterogeneity of lipid dependence within lethal group 3 medulloblastoma

1 week 1 day ago
Medulloblastoma, the most common malignant brain tumor of childhood, exhibits significant biological complexity that demands deeper exploration. Here, we present a large multiomics dataset integrating data from 384 primary medulloblastoma patient samples across five omic layers: CpG methylome, transcriptome, proteome, phosphoproteome, and metabolome, paired with associated clinical metadata. Data integration revealed intertumoral heterogeneity of lipid metabolism across proteomic subtypes....
Flavia Bernardi

Adult outcomes of clinically relevant genomic disorders: A systematic review and meta-analysis

1 week 2 days ago
CONCLUSION: Pooled results suggest that, although there may be elevated prevalence of adult cardiovascular risk conditions, high heterogeneity indicates caution when considering rare deletion syndromes collectively. The paucity of data extending into later adulthood and using age-matched control comparisons supports the need for prospective studies of large, well-phenotyped cohorts to inform adult penetrance of treatable medical diseases in this emerging group of young adults.
Sarah L Malecki

Early COVID-19 and Severity of Subsequent Omicron Infection in Ontario Canada

1 week 4 days ago
We evaluated whether having early COVID-19 reduced the severity of subsequent Omicron infection, assessing activities of daily living (ADL), healthcare utilization and illness duration. Comparisons were made between persons with (1) early COVID-19-compatible illness with a negative test, (2) early lab-confirmed SARS-CoV-2 14-26 months and (3) early lab-confirmed SAR-CoV-2 > 26 months before Omicron infection. Among 261 patients with laboratory-confirmed Omicron, 177 (68%) had COVID-19 in 2020, a...
Caroline Kassee

The development of dynamic networks supporting attentional flexibility

2 weeks ago
Attentional flexibility is a foundational component of human cognition and develops substantially throughout childhood. Although the neural activity supporting attentional flexibility has been well-characterised in adults, its developmental trajectory during childhood and adolescence remains poorly understood. Here, we used magnetoencephalography (MEG) to study brain network dynamics underlying attentional set-shifting. MEG data were collected from 63 participants aged 4 - 19 years, including 30...
Sebastian C Coleman

Soybean maintained immunodiversity during domestication despite a significant loss in genetic diversity

2 weeks ago
Soybean (Glycine max (L.) Merr.) is one of the most economically important crops in the world, but every year, pathogens cause billions of dollars' worth of losses worldwide. The domestication of this critical crop was associated with several severe genetic bottlenecks that resulted in a dramatic loss of genetic diversity (∼50%) relative to its wild progenitor. Although domestication selected for favorable agricultural traits, it is unclear how the reduced genetic diversity affected the immunity...
Yan Lai

Socioeconomic Status Is Associated With Reward Processing, Interleukin 1β, Striatal Connectivity, and Antidepressant Outcomes in Individuals With Major Depressive Disorder: A CAN-BIND-1 Report

2 weeks 1 day ago
CONCLUSIONS: Our results elucidate the role of SES and its negative consequences in altering reward processing and antidepressant treatment efficacy in MDD, corroborating previous literature suggesting that SES significantly impacts health outcomes. Better characterizing the relationship between SES and MDD psychopathology may inform future treatment approaches and intervention development.
Sara Jani

Domestication drives repeated evolution of sexual-asexual life cycle trade-offs in yeast

2 weeks 2 days ago
For thousands of years, humans have domesticated animals and cultivated crops by managing reproduction and selecting for desirable traits. In contrast, microbial domestication has often occurred unintentionally, and the variation of life cycle as well as its impact on genome evolution remain poorly understood. Here, we systematically examined life cycle variation across a diverse panel of 771 diploid Saccharomyces cerevisiae isolates from both wild and domesticated lineages. We identified...
Carmen Becerra-Rodríguez

Application of Large Language Models for Annotating Genes into Reactome Pathways

2 weeks 3 days ago
Reactome is the most comprehensive, open source, open access biological pathway knowledgebase, widely used in the research community. To ensure the highest quality of its content, human pathway data in Reactome is manually curated. However, manual curation is labor-intensive, time-consuming, and increasingly difficult to keep up with the ever-growing biomedical literature. Large language model (LLM)-driven artificial intelligence (AI) technologies are transforming many fields, including...
Guanming Wu